<commit_before>#!/bin/sh -x
# -*- mode: sh; -*-
# $Id$

## script to do all the merges. Change to needs, this is not something very
## general or so. Although you probably could make that using some cheeky
## symlinks

## For each source (ensembl, affymetrix, fgeneh etc.), it needs one big
## collated file (called all.gtf). These files (must) have been created first
## by all-collate.sh.

ens=ensembl/all.gtf
affy=affymetrix/all.gtf
fgenesh=fgenesh/chr_gff/all.gtf 

prefix=igi3

gtf_merge.pl -p $prefix $ens $affy > ens_affy.merge  2> ens_affy.log
gtf_merge.pl -p $prefix $ens $fgenesh > ens_fgenesh.merge 2> ens_fgenesh.log
gtf_merge.pl -p $prefix $affy $fgenesh > affy_fgenesh.merge 2> affy_fgenesh.log
gtf_merge.pl -p $prefix $ens $affy $fgenesh > ens_affy_fgenesh.merge 2>ens_affy_fgenesh.log

### after this, run the statistics on these files using all-stats.sh
<commit_msg>*** empty log message ***<commit_after>#!/bin/sh -x
# -*- mode: sh; -*-
# $Id$

## script to do all the merges. Change to needs, this is not something very
## general or so. Although you probably could make that using some cheeky
## symlinks

## For each source (ensembl, affymetrix, fgeneh etc.), it needs one big
## collated file (called all.gtf). These files (must) have been created first
## by all-collate.sh.

ens=ensembl/all.gtf
affy=affymetrix/all.gtf
fgenesh=fgenesh/chr_gff/all.gtf 
outdir=merges

prefix=igi3

gtf_merge.pl -p $prefix $ens $affy > $outdir/ens_affy.merge  2> ens_affy.log
gtf_merge.pl -p $prefix $ens $fgenesh > $outdir/ens_fgenesh.merge 2> ens_fgenesh.log
gtf_merge.pl -p $prefix $affy $fgenesh > $outdir/affy_fgenesh.merge 2> affy_fgenesh.log
gtf_merge.pl -p $prefix $ens $affy $fgenesh > $outdir/ens_affy_fgenesh.merge 2>ens_affy_fgenesh.log

cd $outdir
for i in *.merge; do
    gzip < $i > $i.gz
done

### after this, run the statistics on these files using all-stats.sh

{'fraction_non_alphanumeric': 0.12314225053078556, 'fraction_numerical': 0.005307855626326964, 'mean_word_length': 4.236111111111111, 'pattern_counts': {'":': 0, '<': 4, '<?xml version=': 0, '>': 20, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7428863', 'n_tokens_mistral': 746, 'n_tokens_neox': 735, 'n_words': 220}