"Concatenating sequence length to another file"

Post #303031776 by RudiC on Tuesday 5th of March 2019 04:59:34 PM

$ wc -cl *.fa | awk '
FILENAME == "-" {sub (".fa", "", $3)
                 T[$3] = $2 - $1
FNR == 1        {IX = FILENAME
                 sub (/_[^_]*\..*$/, "", IX)

                {print FNR, $0, T[IX] > (FILENAME ".new")
' - OFS="\t" fil*pos.txt

$ cf *.new

---------- file_1_pos.txt.new: ----------

1    File_1_pos    253     164    350
2    File_1_pos    738     827    350

---------- file_2_pos.txt.new: ----------

1    File_2_pos    1494    1583    280
2    File_2_pos    1785    1874    280

Copy exactly as given; then mv the ".new" files over the old ".txt" files

EDIT: Given there are any number of .fa files, and each has a corresponding _pos.txt file, you could try
$ wc -cl *.fa |  
awk '
FILENAME == "-" {if ($3 == "total") next
                 sub (".fa", "", $3)
                 T[$3] = $2 - $1
                 ARGV[ARGC++] = $3 "_pos.txt"
FNR == 1        {IX = FILENAME
                 sub (/_[^_]*\..*$/, "", IX)
                {print FNR, $0, T[IX] > (FILENAME ".new")
' - OFS="\t"

Last edited by RudiC; 03-05-2019 at 06:16 PM..

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SQUIZZ(1)							   User Manuals 							 SQUIZZ(1)

squizz - Sequence format checker SYNOPSIS
squizz [-AShlns] [-c format] [-f format] file OPTIONS
Following command line options are allowed: -A Restrict detection/verification to alignment formats (conflict with -S option). -S Restrict detection/verification to sequence formats (conflict with -A option). -c format Convert detected sequence/alignment into format. This option implies strict alignment checking. -f format Assume input format is format. Do not try to detect the format, just verify that the given one is correct. -h Usage display. -l List all supported formats. -n Count and report detected entries. This option is only available when the detection is restricted to a single type (with -A or -S options) and strict checks (without -s option) are enabled. -s Disable strict format checks (enabled by default). DESCRIPTION
squizz is a sequence format file checker, but it has some conversion capabilities too. squizz can detect the most common sequence and alignment formats : * EMBL, FASTA, GCG, GDE, GENBANK, IG, NBRF, PIR (codata), RAW, and SWISSPROT. * CLUSTAL, FASTA, MSF, NEXUS, PHYLIP (interleaved and sequential) and STOCKHOLM. squizz can do some conversions too, if the format the input format is supported. Only 3 types are available : sequence to sequence, align- ment to alignment, and alignment to sequence (the last one, sequence to alignment, require multiple alignments algorithms and cannot be handled with formatting tools). Strict format checks validate the previously detected objects, by making some sanity checks: - sequence strings must exists. - alignment is made of more than one sequence. - alignment sequence strings must have the same length. - alignment sequence names must exists, and be unique. SEE ALSO
seqfmt(5), alifmt(5) AUTHOR
Nicolas Joly (njoly@pasteur.fr), Institut Pasteur. Unix 2009-05-19 SQUIZZ(1)

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