Processing transposon insertion-site deep sequencing (Tn-seq) data

gene_x 0 like s 307 view s

Tags: processing, pipeline

run tpp https://transit.readthedocs.io/en/latest/transit_running.html

#-maxreads 10000 or not_given for take all!
#-primer AGATGTGTATAAGAGACAG     the default primer of Tn5 is TAAGAGACAG!
#-primer-start-window 0,159  set 0,159 as default!

python3 ~/.local/bin/tpp -bwa /usr/bin/bwa -protocol Tn5 -ref WA-314_m.fna -reads1 ./240405_VH00358_89_AAFC5MTM5/kr1/initial_mutants_rep1_S25_R1_001.fastq -reads2 ./240405_VH00358_89_AAFC5MTM5/kr1/initial_mutants_rep1_S25_R2_001.fastq -output 10_chimera -mismatches initial_mutants_rep1 -bwa-alg mem -primer ACCTACCCCNCCGCTCTC -replicon-ids contig_2_10,contig_2_9,contig_2_8,contig_2_7,contig_2_6,contig_2_5,contig_2_3,contig_2_2,contig_5_10,contig_5_11,contig_5_12,contig_5_13,contig_5_15,contig_5_16,contig_5_17,contig_5_18,contig_5_9,contig_5_8,contig_5_7,contig_5_6,contig_5_5,contig_5_4,contig_5_3,contig_5_2,contig_5_1,contig_4_2,contig_4_1,contig_3_59,contig_3_58,contig_3_57,contig_3_56,contig_3_55,contig_3_54,contig_3_53,contig_3_52,contig_3_51,contig_3_50,contig_3_49,contig_3_48,contig_3_47,contig_3_46,contig_3_44,contig_3_43,contig_3_42,contig_3_41,contig_3_40,contig_3_39,contig_3_38,contig_3_37,contig_3_36,contig_3_35,contig_3_34,contig_3_33,contig_3_32,contig_3_31,contig_3_30,contig_3_29,contig_3_28,contig_3_27,contig_3_26,contig_3_25,contig_3_24,contig_3_23,contig_3_22,contig_3_21,contig_3_20,contig_3_17,contig_3_16,contig_3_15,contig_3_14,contig_3_13,contig_3_12,contig_3_11,contig_3_9,contig_3_8,contig_3_7,contig_3_6,contig_3_5,contig_3_3,contig_3_2,contig_3_1,contig_1_48,contig_1_47,contig_1_46,contig_1_45,contig_1_44,contig_1_43,contig_1_42,contig_1_41,contig_1_40,contig_1_39,contig_1_38,contig_1_37,contig_1_34,contig_1_33,contig_1_32,contig_1_31,contig_1_28,contig_1_27,contig_1_26,contig_1_25,contig_1_24,contig_1_22,contig_1_20,contig_1_19,contig_1_18,contig_1_17,contig_1_16,contig_1_15,contig_1_14,contig_1_13,contig_1_12,contig_1_10,contig_1_8,contig_1_7,contig_1_6,contig_1_5,contig_1_4,contig_1_3,contig_1_2,contig_1_1,contig_C8715,contig_C8943,contig_C9371,contig_C8939,contig_C9357,contig_C8991,contig_C9445,contig_C8689
mv tpp.cfg initial_mutants_rep1.tpp.cfg

python3 ~/.local/bin/tpp -bwa /usr/bin/bwa -protocol Tn5 -ref WA-314_m.fna -reads1 ./240405_VH00358_89_AAFC5MTM5/kr1/initial_mutants_rep1_S25_R1_001.fastq -reads2 ./240405_VH00358_89_AAFC5MTM5/kr1/initial_mutants_rep1_S25_R2_001.fastq -output 10 -mismatches initial_mutants_rep1 -bwa-alg mem  -replicon-ids contig_2_10,contig_2_9,contig_2_8,contig_2_7,contig_2_6,contig_2_5,contig_2_3,contig_2_2,contig_5_10,contig_5_11,contig_5_12,contig_5_13,contig_5_15,contig_5_16,contig_5_17,contig_5_18,contig_5_9,contig_5_8,contig_5_7,contig_5_6,contig_5_5,contig_5_4,contig_5_3,contig_5_2,contig_5_1,contig_4_2,contig_4_1,contig_3_59,contig_3_58,contig_3_57,contig_3_56,contig_3_55,contig_3_54,contig_3_53,contig_3_52,contig_3_51,contig_3_50,contig_3_49,contig_3_48,contig_3_47,contig_3_46,contig_3_44,contig_3_43,contig_3_42,contig_3_41,contig_3_40,contig_3_39,contig_3_38,contig_3_37,contig_3_36,contig_3_35,contig_3_34,contig_3_33,contig_3_32,contig_3_31,contig_3_30,contig_3_29,contig_3_28,contig_3_27,contig_3_26,contig_3_25,contig_3_24,contig_3_23,contig_3_22,contig_3_21,contig_3_20,contig_3_17,contig_3_16,contig_3_15,contig_3_14,contig_3_13,contig_3_12,contig_3_11,contig_3_9,contig_3_8,contig_3_7,contig_3_6,contig_3_5,contig_3_3,contig_3_2,contig_3_1,contig_1_48,contig_1_47,contig_1_46,contig_1_45,contig_1_44,contig_1_43,contig_1_42,contig_1_41,contig_1_40,contig_1_39,contig_1_38,contig_1_37,contig_1_34,contig_1_33,contig_1_32,contig_1_31,contig_1_28,contig_1_27,contig_1_26,contig_1_25,contig_1_24,contig_1_22,contig_1_20,contig_1_19,contig_1_18,contig_1_17,contig_1_16,contig_1_15,contig_1_14,contig_1_13,contig_1_12,contig_1_10,contig_1_8,contig_1_7,contig_1_6,contig_1_5,contig_1_4,contig_1_3,contig_1_2,contig_1_1,contig_C8715,contig_C8943,contig_C9371,contig_C8939,contig_C9357,contig_C8991,contig_C9445,contig_C8689
mv tpp.cfg initial_mutants_rep1.tpp.cfg

python3 ~/.local/bin/tpp -bwa /usr/bin/bwa -protocol Tn5 -ref WA-314_m.fna -reads1 ./240405_VH00358_89_AAFC5MTM5/kr3/LB_culture_rep1_S26_R1_001.fastq.gz -reads2 ./240405_VH00358_89_AAFC5MTM5/kr3/LB_culture_rep1_S26_R2_001.fastq.gz -output LB_culture_rep1  -mismatches 1 -bwa-alg mem -replicon-ids contig_2_10,contig_2_9,contig_2_8,contig_2_7,contig_2_6,contig_2_5,contig_2_3,contig_2_2,contig_5_10,contig_5_11,contig_5_12,contig_5_13,contig_5_15,contig_5_16,contig_5_17,contig_5_18,contig_5_9,contig_5_8,contig_5_7,contig_5_6,contig_5_5,contig_5_4,contig_5_3,contig_5_2,contig_5_1,contig_4_2,contig_4_1,contig_3_59,contig_3_58,contig_3_57,contig_3_56,contig_3_55,contig_3_54,contig_3_53,contig_3_52,contig_3_51,contig_3_50,contig_3_49,contig_3_48,contig_3_47,contig_3_46,contig_3_44,contig_3_43,contig_3_42,contig_3_41,contig_3_40,contig_3_39,contig_3_38,contig_3_37,contig_3_36,contig_3_35,contig_3_34,contig_3_33,contig_3_32,contig_3_31,contig_3_30,contig_3_29,contig_3_28,contig_3_27,contig_3_26,contig_3_25,contig_3_24,contig_3_23,contig_3_22,contig_3_21,contig_3_20,contig_3_17,contig_3_16,contig_3_15,contig_3_14,contig_3_13,contig_3_12,contig_3_11,contig_3_9,contig_3_8,contig_3_7,contig_3_6,contig_3_5,contig_3_3,contig_3_2,contig_3_1,contig_1_48,contig_1_47,contig_1_46,contig_1_45,contig_1_44,contig_1_43,contig_1_42,contig_1_41,contig_1_40,contig_1_39,contig_1_38,contig_1_37,contig_1_34,contig_1_33,contig_1_32,contig_1_31,contig_1_28,contig_1_27,contig_1_26,contig_1_25,contig_1_24,contig_1_22,contig_1_20,contig_1_19,contig_1_18,contig_1_17,contig_1_16,contig_1_15,contig_1_14,contig_1_13,contig_1_12,contig_1_10,contig_1_8,contig_1_7,contig_1_6,contig_1_5,contig_1_4,contig_1_3,contig_1_2,contig_1_1,contig_C8715,contig_C8943,contig_C9371,contig_C8939,contig_C9357,contig_C8991,contig_C9445,contig_C8689
mv tpp.cfg LB_culture_rep1.tpp.cfg

python3 ~/.local/bin/tpp -bwa /usr/bin/bwa -protocol Tn5 -ref WA-314_m.fna -reads1 ./240405_VH00358_89_AAFC5MTM5/kr9/intracellular_mutants_24h_rep1_S29_R1_001.fastq.gz -reads2 ./240405_VH00358_89_AAFC5MTM5/kr9/intracellular_mutants_24h_rep1_S29_R2_001.fastq.gz -output intracellular_mutants_24h_rep1 -mismatches 1 -bwa-alg mem -replicon-ids contig_2_10,contig_2_9,contig_2_8,contig_2_7,contig_2_6,contig_2_5,contig_2_3,contig_2_2,contig_5_10,contig_5_11,contig_5_12,contig_5_13,contig_5_15,contig_5_16,contig_5_17,contig_5_18,contig_5_9,contig_5_8,contig_5_7,contig_5_6,contig_5_5,contig_5_4,contig_5_3,contig_5_2,contig_5_1,contig_4_2,contig_4_1,contig_3_59,contig_3_58,contig_3_57,contig_3_56,contig_3_55,contig_3_54,contig_3_53,contig_3_52,contig_3_51,contig_3_50,contig_3_49,contig_3_48,contig_3_47,contig_3_46,contig_3_44,contig_3_43,contig_3_42,contig_3_41,contig_3_40,contig_3_39,contig_3_38,contig_3_37,contig_3_36,contig_3_35,contig_3_34,contig_3_33,contig_3_32,contig_3_31,contig_3_30,contig_3_29,contig_3_28,contig_3_27,contig_3_26,contig_3_25,contig_3_24,contig_3_23,contig_3_22,contig_3_21,contig_3_20,contig_3_17,contig_3_16,contig_3_15,contig_3_14,contig_3_13,contig_3_12,contig_3_11,contig_3_9,contig_3_8,contig_3_7,contig_3_6,contig_3_5,contig_3_3,contig_3_2,contig_3_1,contig_1_48,contig_1_47,contig_1_46,contig_1_45,contig_1_44,contig_1_43,contig_1_42,contig_1_41,contig_1_40,contig_1_39,contig_1_38,contig_1_37,contig_1_34,contig_1_33,contig_1_32,contig_1_31,contig_1_28,contig_1_27,contig_1_26,contig_1_25,contig_1_24,contig_1_22,contig_1_20,contig_1_19,contig_1_18,contig_1_17,contig_1_16,contig_1_15,contig_1_14,contig_1_13,contig_1_12,contig_1_10,contig_1_8,contig_1_7,contig_1_6,contig_1_5,contig_1_4,contig_1_3,contig_1_2,contig_1_1,contig_C8715,contig_C8943,contig_C9371,contig_C8939,contig_C9357,contig_C8991,contig_C9445,contig_C8689
mv tpp.cfg intracellular_mutants_24h_rep1.tpp.cfg

python3 ~/.local/bin/tpp -bwa /usr/bin/bwa -protocol Tn5 -ref WA-314_m.fna -reads1 ./240405_VH00358_89_AAFC5MTM5/kr8/extracellular_mutants_24h_rep2_S28_R1_001.fastq.gz -reads2 ./240405_VH00358_89_AAFC5MTM5/kr8/extracellular_mutants_24h_rep2_S28_R2_001.fastq.gz -output extracellular_mutants_24h_rep2 -mismatches 1 -bwa-alg mem -replicon-ids contig_2_10,contig_2_9,contig_2_8,contig_2_7,contig_2_6,contig_2_5,contig_2_3,contig_2_2,contig_5_10,contig_5_11,contig_5_12,contig_5_13,contig_5_15,contig_5_16,contig_5_17,contig_5_18,contig_5_9,contig_5_8,contig_5_7,contig_5_6,contig_5_5,contig_5_4,contig_5_3,contig_5_2,contig_5_1,contig_4_2,contig_4_1,contig_3_59,contig_3_58,contig_3_57,contig_3_56,contig_3_55,contig_3_54,contig_3_53,contig_3_52,contig_3_51,contig_3_50,contig_3_49,contig_3_48,contig_3_47,contig_3_46,contig_3_44,contig_3_43,contig_3_42,contig_3_41,contig_3_40,contig_3_39,contig_3_38,contig_3_37,contig_3_36,contig_3_35,contig_3_34,contig_3_33,contig_3_32,contig_3_31,contig_3_30,contig_3_29,contig_3_28,contig_3_27,contig_3_26,contig_3_25,contig_3_24,contig_3_23,contig_3_22,contig_3_21,contig_3_20,contig_3_17,contig_3_16,contig_3_15,contig_3_14,contig_3_13,contig_3_12,contig_3_11,contig_3_9,contig_3_8,contig_3_7,contig_3_6,contig_3_5,contig_3_3,contig_3_2,contig_3_1,contig_1_48,contig_1_47,contig_1_46,contig_1_45,contig_1_44,contig_1_43,contig_1_42,contig_1_41,contig_1_40,contig_1_39,contig_1_38,contig_1_37,contig_1_34,contig_1_33,contig_1_32,contig_1_31,contig_1_28,contig_1_27,contig_1_26,contig_1_25,contig_1_24,contig_1_22,contig_1_20,contig_1_19,contig_1_18,contig_1_17,contig_1_16,contig_1_15,contig_1_14,contig_1_13,contig_1_12,contig_1_10,contig_1_8,contig_1_7,contig_1_6,contig_1_5,contig_1_4,contig_1_3,contig_1_2,contig_1_1,contig_C8715,contig_C8943,contig_C9371,contig_C8939,contig_C9357,contig_C8991,contig_C9445,contig_C8689
mv tpp.cfg extracellular_mutants_24h_rep2.tpp.cfg

python3 ~/.local/bin/tpp -bwa /usr/bin/bwa -protocol Tn5 -ref WA-314_m.fna -reads1 ./240405_VH00358_89_AAFC5MTM5/kr6/growthout_control_24h_rep2_S27_R1_001.fastq.gz -reads2 ./240405_VH00358_89_AAFC5MTM5/kr6/growthout_control_24h_rep2_S27_R2_001.fastq.gz -output growthout_control_24h_rep2 -mismatches 1 -bwa-alg mem -replicon-ids contig_2_10,contig_2_9,contig_2_8,contig_2_7,contig_2_6,contig_2_5,contig_2_3,contig_2_2,contig_5_10,contig_5_11,contig_5_12,contig_5_13,contig_5_15,contig_5_16,contig_5_17,contig_5_18,contig_5_9,contig_5_8,contig_5_7,contig_5_6,contig_5_5,contig_5_4,contig_5_3,contig_5_2,contig_5_1,contig_4_2,contig_4_1,contig_3_59,contig_3_58,contig_3_57,contig_3_56,contig_3_55,contig_3_54,contig_3_53,contig_3_52,contig_3_51,contig_3_50,contig_3_49,contig_3_48,contig_3_47,contig_3_46,contig_3_44,contig_3_43,contig_3_42,contig_3_41,contig_3_40,contig_3_39,contig_3_38,contig_3_37,contig_3_36,contig_3_35,contig_3_34,contig_3_33,contig_3_32,contig_3_31,contig_3_30,contig_3_29,contig_3_28,contig_3_27,contig_3_26,contig_3_25,contig_3_24,contig_3_23,contig_3_22,contig_3_21,contig_3_20,contig_3_17,contig_3_16,contig_3_15,contig_3_14,contig_3_13,contig_3_12,contig_3_11,contig_3_9,contig_3_8,contig_3_7,contig_3_6,contig_3_5,contig_3_3,contig_3_2,contig_3_1,contig_1_48,contig_1_47,contig_1_46,contig_1_45,contig_1_44,contig_1_43,contig_1_42,contig_1_41,contig_1_40,contig_1_39,contig_1_38,contig_1_37,contig_1_34,contig_1_33,contig_1_32,contig_1_31,contig_1_28,contig_1_27,contig_1_26,contig_1_25,contig_1_24,contig_1_22,contig_1_20,contig_1_19,contig_1_18,contig_1_17,contig_1_16,contig_1_15,contig_1_14,contig_1_13,contig_1_12,contig_1_10,contig_1_8,contig_1_7,contig_1_6,contig_1_5,contig_1_4,contig_1_3,contig_1_2,contig_1_1,contig_C8715,contig_C8943,contig_C9371,contig_C8939,contig_C9357,contig_C8991,contig_C9445,contig_C8689
mv tpp.cfg growthout_control_24h_rep2.tpp.cfg

#END

cp initial_mutants_rep1.tn_stats initial_mutants_rep1.tn_stats_
#Delete all general statistics before the table data in initial_mutants_rep1.tn_stats_; delete the content after "# FR_corr (Fwd templates vs. Rev templates):"
sed -i 's/read_count (TA sites only, for Himar1)/read_counts/g' *.tn_stats_
sed -i 's/NZ_mean (among templates)/NZ_mean (mean template count over non-zero TA sites)/g' *.tn_stats_

python3 ../parse_tn_stats.py initial_mutants_rep1.tn_stats_ initial_mutants_rep1.tn_stats.xlsx
python3 ../parse_tn_stats.py LB_culture_rep1.tn_stats_ LB_culture_rep1.tn_stats.xlsx

#calculate the sum of the first and second columns by "=SUM(B2:B130)" and "=SUM(C2:C130)"  441057 and 276060

mkdir initial_mutants_rep1_wig
mv *.wig initial_mutants_rep1_wig/
zip -r initial_mutants_rep1_wig.zip initial_mutants_rep1_wig/

#The counts-files are too big, not nessasary to send:
#~/Tools/csv2xls-0.4/csv_to_xls.py initial_mutants_rep1.tn_stats_ *.counts -d$',' -o initial_mutants_rep1.stats.xls;

#   contig_1_10 699 411
#   contig_1_8  3206    2031
#   contig_1_7  3787    2376
#   contig_1_6  4604    2871
#   contig_1_5  2794    1765
#   contig_1_4  83  58
#   contig_1_3  2944    1882
#   contig_1_2  15446   9678
#   contig_1_1  14391   8954

delete PCR-duplicate for checking if the template counts in tpp are correct

To address the issue of PCR duplicates in paired-end sequencing data (which you referred to as "PCA-duplicate," but I believe you meant "PCR duplicate"), you can use tools designed for post-alignment processing of SAM/BAM files. These tools identify and remove or mark duplicates where both reads of a pair are identical to another pair in the library, often indicating that they are duplicates resulting from PCR amplification rather than unique sequencing events.

Step 0. Install Samtools and Picard Tools for Removing PCR Duplicates: Both Samtools and Picard are widely used for manipulating SAM/BAM files, including removing duplicates. Here's how you can use Picard to remove PCR duplicates:

    conda install -c bioconda picard samtools

Step 1: Convert SAM to BAM and sort the BAM file
If your file is in SAM format, you need to convert it to BAM format first using Samtools; PCR duplicate removal requires that the BAM file be sorted by coordinate. This can be done using Samtools:

    samtools view -Sb initial_mutants_rep1.sam > initial_mutants_rep1.bam
    samtools sort initial_mutants_rep1.bam -o initial_mutants_rep1_sorted.bam
    #557566 + 0 read1
    #557566 + 0 read2
    samtools index initial_mutants_rep1_sorted.bam

    #   contig_1_1  14391   8954
    #@SQ     SN:gi|420257081|ref|NZ_AKKR01000009.1|contig_1_1        LN:84292

    # Extract reads from contig_1_1
    samtools view -b initial_mutants_rep1_sorted.bam "gi|420257081|ref|NZ_AKKR01000009.1|contig_1_1" > contig_1_1.bam
    # Run flagstat on the filtered BAM file
    samtools flagstat contig_1_1.bam
    #16589 + 0 read1
    #16579 + 0 read2

Step 3: Mark or Remove Duplicates Using Picard
Picard Tools can be used to mark duplicates. Here, I'll show you how to remove them:

# -Xmx4g between java and -jar
# java -jar /usr/local/bin/picard.jar
        picard MarkDuplicates \
        I=contig_1_1.bam \
        O=contig_1_1_no_duplicates.bam \
        M=marked_dup_metrics.txt \
        REMOVE_DUPLICATES=true
# ## METRICS CLASS        picard.sam.DuplicationMetrics
#LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED     SECONDARY_OR_SUPPLEMENTARY_RDS  UNMAPPED_READS  UNPAIRED_READ_DUPLICATES        READ_PAIR_DUPLICATES    READ_PAIR_OPTICAL_DUPLICATES    PERCENT_DUPLICATION     ESTIMATED_LIBRARY_SIZE
#Unknown Library 111     16473   81      111     90      6114    0       0.372629        16270

    samtools flagstat contig_1_1_no_duplicates.bam
    #10405 + 0 read1
    #10445 + 0 read2

This command marks duplicates (PCR and optical) and removes them, outputting a file without duplicates. The M option specifies where to write metrics about the duplicates.

Step 3 (Alternatively). Using samtools to Remove Duplicates Directly

Alternatively, if you prefer a simple and fast tool, samtools has a rmdup utility, but it's less versatile compared to Picard:

    samtools rmdup -S input_sorted.bam output_no_duplicates.bam

Note that samtools rmdup is deprecated in recent versions of samtools because it does not handle all edge cases as well as Picard.

Considerations
Read Alignment: Ensure that your reads are aligned correctly and that the SAM/BAM files are error-free before duplicate removal.
Optical vs. PCR Duplicates: Picard differentiates between PCR duplicates (originating from the same fragment of DNA) and optical duplicates (artifacts from the sequencing platform). Ensure that this distinction is clear if relevant for your analysis.
Quality Checks: After removing duplicates, it's wise to perform quality control checks to understand how much of your data was affected by duplicates.

Check how the failed trimmed reads not contain the the transposon:genomic boundary TAAGAGACAG

#-3.1- find read sequences
>VH00358:89:AAFC5MTM5:1:1101:63544:1019_:N:0:TTTCTCTA+CTCGACG
ACCTACCCCNCCGCTCTCATCAACCCAATAACGCAGGCAATCAAGCACCCACTGCATCACATAAGGTTGGCTAAGGCGCAATGTATTGCCACAACCGGTCATGTTGTCATATTCACCCTCAGAGGTGAGCCAGTAGTAGCTGGCATTGTCGATCCCACG
>VH00358:89:AAFC5MTM5:1:1101:63960:1019_:N:0:TTTCTCTA+CTCGACG
CAAAGAGGGGGGCGAAAAGATTTTAAACGATCTTGGCGAAATGAATTTTGAGTTTGTCGTGTGTGACTCACCTGCCGGTATCGAAAGCGGTGCGTTGATGGCACTGTATTTTGCTGACG
>VH00358:89:AAFC5MTM5:1:1101:64150:1019_:N:0:TTTCTCTA+CTCGACG
TCTTTACCGGGGATGGGACGCAAGATCTGCGCGCACTGGAACCGGCTTATGTTTCCTCCGTTGACAGTGGGAATCTGGCTGGGCATTTGATTGTACTGGCCAATACCTGTGAAGAGTGGGCCGCAGAACCCTTAGCGGCCAACGGGGCCAAGGGATTG
>VH00358:89:AAFC5MTM5:1:1101:65400:1019_:N:0:TTTCTCTA+CTCGACG
CACCTACCCCCCAGCTCTCATCAACCACAATTGACGCAACATCAGCTGGCGCCATGGCATTAATAACAAACTGGATGAATGGCCCCTGGGATCAACAGCACGAACAAACCGCCGTGTGGTGCCATCAGTTGCGCGCCGAAGGCCATTGACAGAGCACC
>VH00358:89:AAFC5MTM5:1:1101:62048:1038_:N:0:TTTCTCTA+CTCGACG
CCTACACCCCCGCTCTCATCAACCGCAGCAAAGAAAACGAAAATAATGAAGTCATAAAACTCAAGCGCTCCGCCTAAAGCCGCCAGAGTGAGGGTTTTATAATCTTGCTTATTCAGCCGACGGTTATGAT
>VH00358:89:AAFC5MTM5:1:1101:64623:1038_:N:0:TTTCTCTA+CTCGACG
CCTACACCCCAGCTCTCATCAACCAATAACCAGTCAACATCACTGACATCATGTTGCTGGCAATATTCCAGCAGTGCATCTGGCGCCCAAAAACGCGCGCGATCCCCTGCTCGCTGACTTAATACTTGAGTGGCGGCCTTGCCCGGCCCAGTAACCCA
>VH00358:89:AAFC5MTM5:1:1101:65343:1038_:N:0:TTTCTCTA+CTCGACG
ACCTACCACCAAGCTCTCATCAACCTGAATGGATTGAGGGCTACGCTCCCAGATCTGTTCTGCCAATTGGCGCAGATGGTTATCGGTGCAATACAAATGCACAAATGACAAATCGTCTCTTACATCTCAGCTCGATAAACTGCCCTTTGGCATAATGC
>VH00358:89:AAFC5MTM5:1:1101:63317:1057_:N:0:GTTCTCTA+CTCGACG
GTTGGCGTCCGGCATCTGCATATCACTCATAAAGCGCCTCGATAATCCCACGGATATCCTGGTCGCTAGCTGGGCGCGGGTTGGTGCGCAATGTGAGCTCGGCCAGGGCTGCAGCAATCATATCGGGCAGATGTTGCTGCAATTGGCGCTCATTAACTT
>VH00358:89:AAFC5MTM5:1:1101:63430:1057_:N:0:TTTCTCTA+CTCGACG
GCACTGGAAGAGCCGACTAGCCTCAATACTCTTGAACTGCTACCGGAATTATTTGCCGCCAATATTGCCTCGGTGAAAATTGAAGGGCGTCAGCGCAGCCCGGCTTATGTCAGCCAGGTGGCGAAAGTGTGGCGGCAGGCAATTGACCGCTATCTGGC
>VH00358:89:AAFC5MTM5:1:1101:58299:1076_:N:0:TTTCTCTA+CTCGACG
TAAATAGGCCAGACTTGAAATCACACGATCCGGCCAGCGATT

#-3.2- generate the genomic sequences
blastn -db ../WA-314_m.fna -query initial_mutants_rep1.trimmed1_failed_trim_n20 -out failed_trim_n20_on_yersinia.blastn -evalue 10000 -num_threads 124 -outfmt 6 -max_target_seqs 1

VH00358:89:AAFC5MTM5:1:1101:63544:1019_:N:0:TTTCTCTA+CTCGACG    gi|420260421|ref|NZ_AKKR01000094.1|contig_3_51  100.000 141     0       0       19      159     20552   20692   1.20e-70        261
VH00358:89:AAFC5MTM5:1:1101:63960:1019_:N:0:TTTCTCTA+CTCGACG    gi|420258256|ref|NZ_AKKR01000038.1|contig_1_38  98.319  119     2       0       1       119     43674   43556   3.14e-55        209
VH00358:89:AAFC5MTM5:1:1101:64150:1019_:N:0:TTTCTCTA+CTCGACG    gi|420257402|ref|NZ_AKKR01000018.1|contig_1_12  98.101  158     3       0       1       158     59515   59672   4.26e-75        276
VH00358:89:AAFC5MTM5:1:1101:65400:1019_:N:0:TTTCTCTA+CTCGACG    gi|420260713|ref|NZ_AKKR01000106.1|contig_5_2   100.000 57      0       0       18      74      78361   78417   5.91e-24        106
VH00358:89:AAFC5MTM5:1:1101:62048:1038_:N:0:TTTCTCTA+CTCGACG    gi|420257081|ref|NZ_AKKR01000009.1|contig_1_1   100.000 110     0       0       21      130     78749   78640   1.62e-53        204
VH00358:89:AAFC5MTM5:1:1101:64623:1038_:N:0:TTTCTCTA+CTCGACG    gi|420259377|ref|NZ_AKKR01000067.1|contig_3_23  99.329  149     0       1       10      158     54935   55082   7.13e-73        268
VH00358:89:AAFC5MTM5:1:1101:65343:1038_:N:0:TTTCTCTA+CTCGACG    gi|420258810|ref|NZ_AKKR01000051.1|contig_3_3   99.301  143     1       0       16      158     46439   46581   4.29e-70        259
VH00358:89:AAFC5MTM5:1:1101:63317:1057_:N:0:GTTCTCTA+CTCGACG    gi|420257889|ref|NZ_AKKR01000029.1|contig_1_25  96.226  159     6       0       1       159     36032   36190   1.20e-70        261
VH00358:89:AAFC5MTM5:1:1101:63430:1057_:N:0:TTTCTCTA+CTCGACG    gi|420260713|ref|NZ_AKKR01000106.1|contig_5_2   100.000 158     0       0       1       158     54938   55095   4.23e-80        292
VH00358:89:AAFC5MTM5:1:1101:58299:1076_:N:0:TTTCTCTA+CTCGACG    gi|420259608|ref|NZ_AKKR01000075.1|contig_3_31  97.619  42      1       0       1       42      25535   25576   1.04e-14        73.1

samtools faidx WA-314_m.fna "gi|420260421|ref|NZ_AKKR01000094.1|contig_3_51":20534-20692 > genome_rg_for_read1.fasta
samtools faidx WA-314_m.fna "gi|420258256|ref|NZ_AKKR01000038.1|contig_1_38":43556-43674 > genome_rg_for_read2.fasta
samtools faidx WA-314_m.fna "gi|420257402|ref|NZ_AKKR01000018.1|contig_1_12":59515-59672 > genome_rg_for_read3.fasta
samtools faidx WA-314_m.fna "gi|420260713|ref|NZ_AKKR01000106.1|contig_5_2":78344-78501 > genome_rg_for_read4.fasta
samtools faidx WA-314_m.fna "gi|420257081|ref|NZ_AKKR01000009.1|contig_1_1":78640-78769 > genome_rg_for_read5.fasta
samtools faidx WA-314_m.fna "gi|420259377|ref|NZ_AKKR01000067.1|contig_3_23":54926-55082 > genome_rg_for_read6.fasta
samtools faidx WA-314_m.fna "gi|420258810|ref|NZ_AKKR01000051.1|contig_3_3":46424-46581 > genome_rg_for_read7.fasta
samtools faidx WA-314_m.fna "gi|420257889|ref|NZ_AKKR01000029.1|contig_1_25":36032-36190 > genome_rg_for_read8.fasta
samtools faidx WA-314_m.fna "gi|420260713|ref|NZ_AKKR01000106.1|contig_5_2":54938-55095 > genome_rg_for_read9.fasta
samtools faidx WA-314_m.fna "gi|420259608|ref|NZ_AKKR01000075.1|contig_3_31":25535-25576 > genome_rg_for_read10.fasta

#-3.3- transposon amplicon start sequence
>Transposon_ampli_start
ACCTACAACAAAGCTCTCATCAAC CGTGGCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTCAGGGTTGAGATGTGTA TAAGAGACAG

#-3.4- generate 10 failed_${read}_group.fasta and multiple align them
for read in read1 read2 read3 read4 read5 read6 read7 read8 read9 read10; do
cat failed_${read}.fasta genome_rg_for_${read}.fasta transposon_ampli_start.fasta > failed_${read}_group.fasta
mafft --adjustdirection --clustalout failed_${read}_group.fasta > failed_${read}_group.aln
done

cat failed_read1_group.aln failed_read2_group.aln failed_read3_group.aln failed_read4_group.aln failed_read5_group.aln failed_read6_group.aln failed_read7_group.aln failed_read8_group.aln failed_read9_group.aln failed_read10_group.aln > failed_reads_group.aln

#-3.5- show the results in checking_failed_reads.pdf

Source code of parse_tn_stats.py used in the point 1.

import argparse
import pandas as pd

def parse_tn_stats_detailed(file_path):
    with open(file_path, 'r') as file:
        lines = file.readlines()

    print("Number of lines read:", len(lines))
    if lines:
        print("First few lines:", lines[:10])

    metrics_df = pd.DataFrame()
    current_metric = None
    metric_data = {}

    for line in lines:
        if line.startswith('# ') and not line.startswith('#  '):  # Ensure it's not a contig data line  # Metric definition
            if current_metric and metric_data:
                # Save data before starting new metric
                for contig, value in metric_data.items():
                    metrics_df.at[contig, current_metric] = value
                metric_data = {}
            # Extract the metric name
            current_metric = line.split(':')[0].strip('# ')
            print("Processing new metric:", current_metric)  # Debug output
        else:  # Data lines for contigs under the current metric
            parts = line.strip().split(':')
            contig = parts[0].strip()
            value = parts[1].strip()
            try:
                value = float(value) if value.lower() != 'nan' else pd.NA
            except ValueError:
                value = pd.NA  # In case of conversion failure
            metric_data[contig] = value

    # Capture the last metric data after finishing all lines
    if current_metric and metric_data:
        for contig, value in metric_data.items():
            metrics_df.at[contig, current_metric] = value

    metrics_df.fillna(value=pd.NA, inplace=True)
    return metrics_df

def main():
    parser = argparse.ArgumentParser(description="Parse detailed TN stats from a file and output to Excel.")
    parser.add_argument("input_file", help="Input file path for TN stats.")
    parser.add_argument("output_file", help="Output Excel file path.")
    args = parser.parse_args()

    # Parse the detailed metrics from the provided file path
    detailed_metrics_df = parse_tn_stats_detailed(args.input_file)

    # Save the DataFrame to an Excel file
    with pd.ExcelWriter(args.output_file, engine='openpyxl') as writer:
        detailed_metrics_df.to_excel(writer, sheet_name='Detailed Metrics')

    print(f"Final DataFrame saved to Excel: {args.output_file}")

if __name__ == "__main__":
    main()

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